Implications of genetic entropy. (1-3)

Implications 1: Genesis and decay. (See Figure 8)
BQ: Using everything we've learned about genetics, we're going ask, "What are some important implications of genetic entropy?" Well, we have seen that molecular evidence is 180 degrees off from evolutionary theory. Instead, as we go backward in time, useful information increases, and harmful mutations decrease. 

Remember how we see improvements as we go back in time instead of forward? In the Bible, people in old testament times were recorded as having longer life spans the further back in history one looked. Holladay and Watt ran numerical simulations on the listed ages of these people vs. the dates the timelines compute to, and found that there was an exponential decay curve in lifespans. The correlation coefficient with Biblical data was shockingly close (.94), and the formula of best fit was y=386.6835(e^-0.00462214x)+70.065.

This is unexpected and amazing because it is a biological decay curve. Either the data was recorded faithfully by the writer of Genesis, or he fabricated the info using advanced mathematics and a desire to show exponential decay. But why would someone want to show such a decay curve, especially without knowledge of genetics and mutations, and with no understanding of such advanced math? Is this an elaborate, stone-age fraud? Given that no reason is given for listing the numbers in the Bible, and the impossibility of  someone at time having that sort of foreknowledge, it can't be be a fraud. Empirical evidence supports genetic entropy, while philosophical hand-waving about natural selection presents nothing. I'll leave the conclusion up to you—why does the Bible model genetic entropy in the same way that our molecular makeup does? 
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Figure 8

Implications 2: Size of the genome.
BQ: In our look at the implications of genetic entropy, we can see that we have a problem: mutations accumulate at a rate of 600-6000 per generation. But wait, we have 6 billion nucleotides, so losing one ten-millionth of our information per generation isn't that bad, is it?

Well, as it turns out, out genome is much like a computer program. Computer programs can be millions and billions of bytes in size, yet can fail because of a single error. Much like like us, most sturdy programs can continue to function even with multiple errors. Luckily for us, our genome is incredibly robust and able to withstand many, many errors. However, in the evolutionary timespan since we allegedly evolved from chimps, we would have accumulated a minimum of 90,000,000 errors. It is inconceivable that we would still be functional with a 3% data loss in the genome. 

Like any information, there must be an engineer/designer for it, and also like any information, it WILL decay. Consider the Chinese telephone game you played when you were a child: as the whisper was passed down the line, it was changed, and the net information was lost and distorted. 

The very existence of the genome is a mystery in evolutionary terms. Information and polyfunctional complexity which far surpass our ability to understand are programmed into space impossible to see with the naked eye. It should be obvious that our genome did not arise spontaneously, which leads to only one conclusion: it is an engineered masterpiece. The engineer has been known since ancient times. He has written the book using genetic language of who we are. It is perfect in every sense to see Acts 3:15 describe Him as "the Author of life," as that is exactly what He is.
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Implications 3: The Titanic is doomed.
BQ: The messages on genetics so far have been two-fold, but a major portion of them focus on the fact that we are on board a sinking ship. It is horrific to think that every species is eroding away, like a sand castle on a beach, a beautiful creation that is slowly losing its form. Yet it is necessary to KNOW the bad news in order to know how to respond. 

So how does someone respond? If the evidence is ignored, there is only one response: death and decay. Morality becomes meaningless other than to live physically a little bit longer, to avoid an early death. If your hope is in a sinking ship, your best response is merely to be on the last part that sinks.

But if the logical evidence is followed, and if you recognize that there is an "Author of life," as Acts 3:15 states, suddenly there is a lifeboat! There is no need to go down with the sinking ship. You see, apart from Jesus, there is no hope. There is only the inevitability of death. Science and physics cannot conquer it, but rather ensure it. Yet God made you alive. He made the heavens and the earth in the first place, so He can make you alive again, and when He promises a new heaven and new earth, He is able to meet that promise. Because He rose from the dead, we can also have that hope. And apart from that, there is no hope. 
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Can natural selection create novel genetic info? (Pt 4-7)

Can natural selection create: Part 4: Waiting for other mutations: Lots of colons!
BQ: We are considering the question, "Can natural selection CREATE even a single useful gene?" Remember, it's quite easy to modify existing genetic code, and your body does all the time. That's why we get cancer. It's why we are all, in fact, unique mutants. But can natural selection CREATE novel information? 

It took us 12,000,000 years to stabilize our first desired mutation, and we saw that such presented a large problem with the evolutionary timeline. But keep in mind, it took us that long to encode a SINGLE useful nucleotide. Genes are at a minimum 1000 nucleotides in length, and that's about 50 times too generous, as we're ignoring regulating elements and introns. 

However, to give ourselves the best chance of creating new, useful information, we're setting up this advantage. We'll call it a nice, linear, piece-by-piece process. Our first change took 12,000,000 years, and now we need to do it at least 1,000 more times, and it has to be useful. How long will that take? Well, multiply 12,000,000 times 1000 more times and you get, 12,000,000,000 years. That's a little bit under the time that the Big Bang took place, and we just made one single, useful gene, in a world with no harmful mutations and perfect selection. 

Tomorrow, we need to look at even MORE factors that we're leaving out. Also, remember, this is making a new, useful gene only 1000 nucleotides long. Our genome is composed of 6,000,000,000. How long would it take to make such a genome if it takes so long just to create one new gene? And, from a while ago, we found out that creating the first "life" exceeds the probabilistic resources of the entire universe for its stated "life"span. From that we saw that M-theory was a fallback, because if we have multiple (in this case, infinite) universes, then such an infinitely small (by definition, impossible) chance of it happening would have to take place. Oh, and in one universe you, dear reader, are the Pope, and have a miniature llama as a pet.

(F. Hoyle, Mathematics of Evolution. M. Lynch, J. Conery, R. Burger, Mutation accumulation and the extinction of small populations. J. Neel, The rate with which spontaneous mutation alters the electrophoretic mobility of polypeptides. J. Adell, J. Dopazo, Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates.)
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Can natural selection create: Part 5: Surprisingly slow.
BQ: We are continuing to answer the question, "Can natural selection create even a single useful gene?" Yesterday we "made" our first cool, new nucleotide. It took us just this side of forever to do so. What we didn't mention is that the human genome occurs in large "chunks" of between 20K-40K nucleotides within which we have no recombination. This means that the nucleotides are not moving around. Essentially, this reduces the probability that we can easily create the gene, and adds even more billions of years into the calculation. (The nucleotide mutations have to occur in such a way that they adjoin each other.) 

But now we have our mutant nucleotide and are trying to get it to "survive" reproduction and to be passed on; since we have 20K possible nucleotide alternatives within our population of 10K, we have a tough goal. We want to go from two copies of the mutation in the population to four, and then more from there. If the mutation managed to be reproduced at 10% per generation (this is an awesome mutation that turns you into a supermodel and gives you just the best qualities ever), it would take us ~105 generations (2100 years) to increase from 1 to 20K copies. (1.1^105=20K). 

The problem is these advantages are unrealistic. According to Patterson in "Evolution," a recessive beneficial mutation that would increase fitness by 1% would take 100,000 generations to fix. Haldane in, "The cost of natural selection," estimated that the most nominal time for fixation of a beneficial new mutation to take place is at least 300 generations, or >6000 years. This is called, "Haldane's dilemma," as it is so slow that it means there is effectively no selection taking place. 

But if we can create one new nucleotide in 6000 years, can't we create a new gene in 6 million, the time since we supposedly evolved from apes? No. Haldane's dilemma concerns unlinked, non-adjacent mutations. For 1000 specific, adjacent mutations, it would take well over 6 billion years; furthermore, selecting for one nucleotide reduces our ability to select for others, which is called "selection interference." 

We can conclude from all this that we cannot create even one new gene within our evolutionary timeframe, even without harmful mutations to boot. 

Coming up, we'll look at the implications of endless fitness valleys, deleterious mutations, and poly-constrained mutations, all in our attempt to make evolution act the way "it's supposed to." We have about two or three questions left on this, and they should be easier to understand. 
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Can natural selection create: Part 6: Inferiority and fitness.
BQ: Continuing to see if natural selection can create a single useful gene, we now need to look at the conclusion of some known facts that we've left out. We know that man and ape differ by approximately 150,000,000 nucleotides. As we've seen, as a percentage, that's not too much, but as a genetic change in raw nucleotide numbers, that's massive. These changes account for at least 40,000,000 mutations. 

If we assume that man came from chimp-like creatures, there must have been 20,000,000 nucleotide fixations within the human lineage (40,000,000/2), but we found out yesterday that natural selection could maximally have accounted for ~1000 of these in 6 million years, and they would have been non-sequential. What does this mean? It means that the rest would have been fixed by random drift, not a natural "enhancement" by selection, which would make them...you guessed it, nearly-neutral but HARMFUL mutations. We'd have on the best of days 1000 "good" mutations and millions of harmful ones, which would mean that man DEVOLVED from chimps! In fact, we'd be statistically dead!

Before we move on to poly-constrained DNA tomorrow, we need to briefly consider fitness valleys. Evolutionists can show that the creation of a new gene takes a great deal of experimentation. When the gene is being developed, there is a period of time when the species' fitness declines. This is called a "fitness valley." A partially-completed gene is not neutral, and it's not helpful...it's harmful. The species, then, must be harmed in order to be enhanced. We can imagine a situation where a species could survive fitness valleys if they were rare and short-lived, but continuous evolutionarily-positive innovation of novel genes would mean continuous, harmful fitness valleys, or one longer valley with a negative trajectory. Indefinitely number, indefinitely long fitness valleys ultimately would destroy all species. 
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Can natural selection create: Part 7: Polyfunctional DNA (See Figure 5—Polyfunctional Complexity)
Continuing to see if natural selection can create a single useful gene, we now need to look at the conclusion of some known facts that we've left out. We know that man and ape differ by approximately 150,000,000 nucleotides. As we've seen, as a percentage, that's not too much, but as a genetic change in raw nucleotide numbers, that's massive. These changes account for at least 40,000,000 mutations. 

If we assume that man came from chimp-like creatures, there must have been 20,000,000 nucleotide fixations within the human lineage (40,000,000/2), but we found out yesterday that natural selection could maximally have accounted for ~1000 of these in 6 million years, and they would have been non-sequential. What does this mean? It means that the rest would have been fixed by random drift, not a natural "enhancement" by selection, which would make them...you guessed it, nearly-neutral but HARMFUL mutations. We'd have on the best of days 1000 "good" mutations and millions of harmful ones, which would mean that man DEVOLVED from chimps! In fact, we'd be statistically dead!

Before we move on to poly-constrained DNA tomorrow, we need to briefly consider fitness valleys. Evolutionists can show that the creation of a new gene takes a great deal of experimentation. When the gene is being developed, there is a period of time when the species' fitness declines. This is called a "fitness valley." A partially-completed gene is not neutral, and it's not helpful...it's harmful. The species, then, must be harmed in order to be enhanced. We can imagine a situation where a species could survive fitness valleys if they were rare and short-lived, but continuous evolutionarily-positive innovation of novel genes would mean continuous, harmful fitness valleys, or one longer valley with a negative trajectory. Indefinitely number, indefinitely long fitness valleys ultimately would destroy all species. 
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Figure 5—Polyfunctional Complexity

Can natural selection create novel genetic info? (Pt 1-3)

Can natural selection create: Part 1? (See Figure 1—Genes; Figure 2—Irreducibly complex)
BQ: Based on the independent research of Haldane, Gabriel, Tishkoff, Verrelli, Crow, Kimura, ReMine, and  other scientists, I'd like to start a deeper look at natural selection’s ability to create useful information. We'll start off with the question, "can natural selection create even a single useful gene?"  Furthermore, we'll work our way slowly, recalling past research and questions, and give ourselves a favorable scenario to create an "origin of species."  

Let's take a look at defining our first desirable mutation by asking, "is any particular nucleotide more valuable than any other?"

A: By itself, no nucleotide (A, T, C, G) has any more value than any other, in the same way that no letter in the English alphabet has any particular value outside of the letters around it. That is, a letter's value is defined by the context we find it in, and so are nucleotides. A change to a single letter in this sentence can only be evaluated by the surrounding letters. 

From this, we see an example of irreducible complexity. Irreducible complexity presents a problem for evolutionary thought, though circularly many try to arm-wave it away with the all-powerful, "natural selection." By irreducible complexity, we mean, "a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition non-functional.’ (Behe)

If we look at the problem with creating these sentences (the DNA of this BQ), we'll see we have a very basic bit of irreducible complexity. To create new information, we need to select for our first beneficial mutation, but...we can only define the value of the nucleotide/mutation as compared to its nucleotide neighbors. By changing the nucleotide, we inherently also change the overall meaning of the neighbors; we have therefore created a circular paradox as we keep destroying the context on which we are trying to build. 

Tomorrow, we'll start off from here and look at the problem of fundamental inter-relationships of nucleotides, known as "epistasis." If you have any questions at this point, shoot me a message and I'll be glad to explain it better. :)
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Figure 1—Genes

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Figure 2—Irreducibly complex

Can natural selection create: Part 2. (See Figure 3—Epistasis)

BQ: We are considering the question, "Can natural selection create even a single useful gene?" We are giving ourselves a massive advantage by assuming that we have no negative mutations ever (IRL, the neg/pos ratio of mutations is pretty much "vast-to-none"). Yesterday we learned that no nucleotide (DNA building block) is more useful than another by itself. We also learned that they are only useful in the context of the other "building blocks" around them, and that any mutation inherently affects context. Therefore, we inherently have irreducibly complex DNA.

Today we need some background information clarified, so we're going to look at epistasis. Epistasis is a problem with the fundamental inter-relationship between nucleotides. Essentially, this inter-relationship between nucleotides is infinitely complex. When we define epistasis, we say that, "Different mutations that affect the same trait often interact, so a harmful mutation may be much more or less harmful depending on the absence or presence of other mutations." This "noise" in the DNA makes natural selection of genetic benefits almost impossible, like trying to get only internet with Comcast, yet having to buy a bundle with overpriced phone and TV. Genomes are a package deal; we can't just take that nice internet deal for super cheap. 

Genetic language, like any language, is not a product of chance. Having letters randomly fall into meaningful places is not statistically feasible (in fact, as we saw before, it exceeds the probabilistic resources of the entire universe), and the same can be said for our genetic language. We know from computational models than strings of nucleotides (and just dozens of them, not billions as found in our DNA) cannot randomly fall into place, but we're going to look and see if we could accomplish this one nucleotide at a time, giving ourselves another advantage.

With this background information out of the way, tomorrow we'll examine the timespan we'd have to have for our first mutation within human evolution to become "fixed," and we're going to give ourselves the benefit of having no "package" deal with mutations, though epistatically we know that we would HAVE to have many bad mutations attached to any "improvement mutation." We'll use the assumed population model proposed by evolutionary theory and see how long it'd take us if everything was perfectly in our favor.  

Attached is a picture I made to help you visualize what we're talking about when we say "epistasis." 
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Figure 3 —Epistasis

Can natural selection create: Part 3, The waiting game. (See Figure 4—Extrinsic Factors.)
BQ: We now know what the concept of irreducible complexity is as well as the tough problem of epistasis. We continue to move forward with our question, "can natural selection create even a single useful gene?" Today, we're assuming no harmful mutations exist or would exist, and that we have a pristine human population to pull from, using the evolutionarily accepted figure of about 10,000 individuals.

The mutation rate for any given nucleotide is about 1 chance in 30,000,000. So if we assume 100 mutations per person per generation, we need about 3000 generations, or 60,000 years, to expect a specific nucleotide within our population of 10,000 to mutate. About 66% of the time, it will mutate into the "wrong" building block. So for a specific site to get a beneficial mutation, it'll take about 3x as long, or 120,000 years. Once we do get it, we need to "fix" it—that is, make sure that all individuals will have two copies.

Our challenge is then genetic drift. That is, a mutation needs to be exceedingly noticeable and beneficial to counteract the extrinsic factors and genetic noise. In other words, it's hard to "keep the mutation ball rolling," because most reproduction will not be based upon this one beneficial mutation, but rather other aspects. So perhaps the mutation gives our individual nice abs, but because of the way he was "raised," he is obnoxious and no other individual mates with him to produce offspring which might pass the mutation on. According to population geneticists, the new mutation has 1 chance in 20,000 (total number of non-mutant, location-specific nucleotides present in the population) of not being lost via this genetic drift.

At least 99% of the time, even a good beneficial mutation will be lost via drift. So even a BENEFICIAL mutation needs to happen about 100 times before it "sticks around." On average, then, we would need 120,000 years times 100, or 12,000,000 years to stabilize a first desired genetic mutation. But remember, this is ONE nucleotide segment, and we need MANY of these to build just one desired mutational gene. It supposedly took us 6,000,000 years to evolve from ape-like creatures, but we can see that we can only realistically expect to fix one good mutation in twice that long, and that's without harmful mutations thrown in.

Next, we'll look at the wait for other mutations in building our gene, because one nucleotide base pair does not a gene make.
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Figure 4—Extrinsic Factors

Junk DNA?

Junk DNA?
BQ: When I was in school, I was taught that most of my DNA was "junk DNA" that had no purpose. It was just the vestigial remnant of a copying, mutational process that was "evolution." Is this true, and why is it important?

A: Deleterious (harmful) mutations were said to be rare, as much of the genome was considered "filler" that served no purpose. This meant that the number of mutations could be high in reproductive populations, as the probability of the mutations having affected "useful" DNA was quite low. Thus, geneticists reasoned, most mutations would be "neutral," causing neither harm nor gain. 

In June of 2007, ENCODE, an international consortium of genome scientists, put out 29 research papers. Stunningly, it was discovered that the human genome is vastly more complex than just a simple "zipper" of nucleotides. Basically, the entire genome is transcribed bi-directionally! So not only is the genome not full of "non-functioning junk DNA," but this "junk" is actually poly-functional informational coding! One combination of nucleotides has not just one functional role, but multiple. This means that our genome's functionality exceeds 100%! 

What does this mean? All these "neutral mutations," which evolution "needed to prevent error catastrophe arising from mutational meltdown," are actually not neutral at all, but instead harmful--and each single mutation is harmful on multiple levels. Since natural selection must take the entire package (that is, all 6 billion nucleotides, not just the ones it "likes"), any one good mutation is going to be coupled with hundreds to thousands of times as many harmful mutations! Biochemically, evolution just keeps striking out. Not only can it not explain how information for genomes became present, but it can't even explain how information can REMAIN there! 

(See also: Behe, Darwin's Black Box: The Biochemical Challenge to Evolution, Howell et al., "Evolution of Human mtDNA: How rapid does human mitochondrial genome evolve," Loewe, L., "Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA.") 
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